"When you solve the riddle, it opens up a room on the left hand side of the tower. That room contains the final hand"
Oh if you mean the room with the like dark purple spikey hand then yeah I got that one. But that hand opens a room on the other site of the tower and there's another grave that needs to be opened in that room, for which I cannot find the hand.
Honestly I wasn't really paying attention to when the item position bug happened which makes it not a very good bug report I guess. Maybe it has nothing to do with exiting the game. Having something to do with the legendary tree sounds plausible, I never used a memory disk so it's definitely not that.